Figure 2

Footprinting the Ka/Ks ratio in primate BRCA1. A DNA alignment of five partial primate sequences from exon 11 of BRCA1 footprinted for adaptive evolution. A codon model of evolution with a model parameter for replacement changes[25] was "footprinted" in 300 base (100 codon) windows and 30 base steps. Red lines indicate the 95% confidence interval for the omega replacement parameter that is an estimate of the Ka/Ks ratio. Ka/Ks > 1 is indicative of adaptive evolution. Two regions (around 1850 and 2400 bp) have 95% confidence intervals for omega that do not include 1, suggesting adaptive evolution is occurring within them. Note that although plotted as single lines in the middle of the window range the 300 bp windows overlap and a single region or site can affect the parameter estimate for multiple adjacent windows. Annotations of protein-protein interaction domains (blue boxes) and phosphorylation sites (red diamonds) are derived from Deng[33]. Sequences: Human 961-3798 of NM007294, Chimpanzee 150-2987 of AF019075, Gorilla 150-2987 of AF019076, Orangutan 150-2987 of AF019077 and Rhesus 150-2984 of AF019078. Scale is in bases and refers to gapped alignment positions.